[petsc-users] Can't expand MemType 1: jcol 16104
Satish Balay
balay at mcs.anl.gov
Thu Jul 30 15:51:57 CDT 2015
I've updated petsc to use v4.1. The changes are in branch
'balay/update-superlu_dist-4.1' - and merged to 'next' for now.
Satish
On Wed, 29 Jul 2015, Xiaoye S. Li wrote:
> Thanks for quick update. In the new tarball, I have already removed the
> junk files, as pointed out by Satish.
>
> Sherry
>
> On Wed, Jul 29, 2015 at 8:36 AM, Hong <hzhang at mcs.anl.gov> wrote:
>
> > Sherry,
> > With your bugfix, superlu_dist-4.1 works now:
> >
> > petsc/src/ksp/ksp/examples/tutorials (master)
> > $ mpiexec -n 4 ./ex10 -f0 Amat_binary.m -rhs 0 -pc_type lu
> > -pc_factor_mat_solver_package superlu_dist -mat_superlu_dist_parsymbfact
> > Number of iterations = 1
> > Residual norm 2.11605e-11
> >
> > Once you address Satish's request, we'll update petsc interface to this
> > version of superlu_dist.
> >
> > Anthony:
> > Please download the latest superlu_dist-v4.1,
> > then configure petsc with
> > '--download-superlu_dist=superlu_dist_4.1.tar.gz'
> >
> > Hong
> >
> > On Tue, Jul 28, 2015 at 11:11 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> >
> >> Sherry,
> >>
> >> One minor issue with the tarball. I see the following new files in the
> >> v4.1 tarball
> >> [when comparing it with v4.0]. Some of these files are perhaps junk files
> >> - and can
> >> be removed from the tarball?
> >>
> >> EXAMPLE/dscatter.c.bak
> >> EXAMPLE/g10.cua
> >> EXAMPLE/g4.cua
> >> EXAMPLE/g4.postorder.eps
> >> EXAMPLE/g4.rua
> >> EXAMPLE/g4_postorder.jpg
> >> EXAMPLE/hostname
> >> EXAMPLE/pdgssvx.c
> >> EXAMPLE/pdgstrf2.c
> >> EXAMPLE/pwd
> >> EXAMPLE/pzgstrf2.c
> >> EXAMPLE/pzgstrf_v3.3.c
> >> EXAMPLE/pzutil.c
> >> EXAMPLE/test.bat
> >> EXAMPLE/test.cpu.bat
> >> EXAMPLE/test.err
> >> EXAMPLE/test.err.1
> >> EXAMPLE/zlook_ahead_update.c
> >> FORTRAN/make.out
> >> FORTRAN/zcreate_dist_matrix.c
> >> MAKE_INC/make.xc30
> >> SRC/int_t
> >> SRC/lnbrow
> >> SRC/make.out
> >> SRC/rnbrow
> >> SRC/temp
> >> SRC/temp1
> >>
> >>
> >> Thanks,
> >> Satish
> >>
> >>
> >> On Tue, 28 Jul 2015, Xiaoye S. Li wrote:
> >>
> >> > I am checking v4.1 now. I'll let you know when I fixed the problem.
> >> >
> >> > Sherry
> >> >
> >> > On Tue, Jul 28, 2015 at 8:27 AM, Hong <hzhang at mcs.anl.gov> wrote:
> >> >
> >> > > Sherry,
> >> > > I tested with superlu_dist v4.1. The extra printings are gone, but
> >> hang
> >> > > remains.
> >> > > It hangs at
> >> > >
> >> > > #5 0x00007fde5af1c818 in PMPI_Wait (request=0xb6e4e0,
> >> > > status=0x7fff9cd83d60)
> >> > > at src/mpi/pt2pt/wait.c:168
> >> > > #6 0x00007fde602dd635 in pzgstrf (options=0x9202f0, m=4900, n=4900,
> >> > > anorm=13.738475134194639, LUstruct=0x9203c8, grid=0x9202c8,
> >> > > stat=0x7fff9cd84880, info=0x7fff9cd848bc) at pzgstrf.c:1308
> >> > >
> >> > > if (recv_req[0] != MPI_REQUEST_NULL) {
> >> > > --> MPI_Wait (&recv_req[0], &status);
> >> > >
> >> > > We will update petsc interface to superlu_dist v4.1.
> >> > >
> >> > > Hong
> >> > >
> >> > >
> >> > > On Mon, Jul 27, 2015 at 11:33 PM, Xiaoye S. Li <xsli at lbl.gov> wrote:
> >> > >
> >> > >> Hong,
> >> > >> Thanks for trying out.
> >> > >> The extra printings are not properly guarded by the print level. I
> >> will
> >> > >> fix that. I will look into the hang problem soon.
> >> > >>
> >> > >> Sherry
> >> > >>
> >> > >>
> >> > >> On Mon, Jul 27, 2015 at 7:50 PM, Hong <hzhang at mcs.anl.gov> wrote:
> >> > >>
> >> > >>> Sherry,
> >> > >>>
> >> > >>> I can repeat hang using petsc/src/ksp/ksp/examples/tutorials/ex10.c:
> >> > >>> mpiexec -n 4 ./ex10 -f0 /homes/hzhang/tmp/Amat_binary.m -rhs 0
> >> -pc_type
> >> > >>> lu -pc_factor_mat_solver_package superlu_dist
> >> -mat_superlu_dist_parsymbfact
> >> > >>> ...
> >> > >>> .. Starting with 1 OpenMP threads
> >> > >>> [0] .. BIG U size 1342464
> >> > >>> [0] .. BIG V size 131072
> >> > >>> Max row size is 1311
> >> > >>> Using buffer_size of 5000000
> >> > >>> Threads per process 1
> >> > >>> ...
> >> > >>>
> >> > >>> using a debugger (with petsc option '-start_in_debugger'), I find
> >> that
> >> > >>> hang occurs at
> >> > >>> #0 0x00007f117d870998 in __GI___poll (fds=0x20da750, nfds=4,
> >> > >>> timeout=<optimized out>, timeout at entry=-1)
> >> > >>> at ../sysdeps/unix/sysv/linux/poll.c:83
> >> > >>> #1 0x00007f117de9f7de in MPIDU_Sock_wait (sock_set=0x20da550,
> >> > >>> millisecond_timeout=millisecond_timeout at entry=-1,
> >> > >>> eventp=eventp at entry=0x7fff654930b0)
> >> > >>> at src/mpid/common/sock/poll/sock_wait.i:123
> >> > >>> #2 0x00007f117de898b8 in MPIDI_CH3i_Progress_wait (
> >> > >>> progress_state=0x7fff65493120)
> >> > >>> at src/mpid/ch3/channels/sock/src/ch3_progress.c:218
> >> > >>> #3 MPIDI_CH3I_Progress (blocking=blocking at entry=1,
> >> > >>> state=state at entry=0x7fff65493120)
> >> > >>> at src/mpid/ch3/channels/sock/src/ch3_progress.c:921
> >> > >>> #4 0x00007f117de1a559 in MPIR_Wait_impl (request=request at entry
> >> > >>> =0x262df90,
> >> > >>> status=status at entry=0x7fff65493390) at src/mpi/pt2pt/wait.c:67
> >> > >>> #5 0x00007f117de1a818 in PMPI_Wait (request=0x262df90,
> >> > >>> status=0x7fff65493390)
> >> > >>> at src/mpi/pt2pt/wait.c:168
> >> > >>> #6 0x00007f11831da557 in pzgstrf (options=0x23dfda0, m=4900,
> >> n=4900,
> >> > >>> anorm=13.738475134194639, LUstruct=0x23dfe78, grid=0x23dfd78,
> >> > >>> stat=0x7fff65493ea0, info=0x7fff65493edc) at pzgstrf.c:1308
> >> > >>>
> >> > >>> #7 0x00007f11831bf3bd in pzgssvx (options=0x23dfda0, A=0x23dfe30,
> >> > >>> ScalePermstruct=0x23dfe50, B=0x0, ldb=1225, nrhs=0,
> >> grid=0x23dfd78,
> >> > >>> LUstruct=0x23dfe78, SOLVEstruct=0x23dfe98, berr=0x0,
> >> > >>> stat=0x7fff65493ea0,
> >> > >>> ---Type <return> to continue, or q <return> to quit---
> >> > >>> info=0x7fff65493edc) at pzgssvx.c:1063
> >> > >>>
> >> > >>> #8 0x00007f11825c2340 in MatLUFactorNumeric_SuperLU_DIST
> >> (F=0x23a0110,
> >> > >>> A=0x21bb7e0, info=0x2355068)
> >> > >>> at
> >> > >>>
> >> /sandbox/hzhang/petsc/src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c:411
> >> > >>> #9 0x00007f1181c6c567 in MatLUFactorNumeric (fact=0x23a0110,
> >> > >>> mat=0x21bb7e0,
> >> > >>> info=0x2355068) at
> >> > >>> /sandbox/hzhang/petsc/src/mat/interface/matrix.c:2946
> >> > >>> #10 0x00007f1182a56489 in PCSetUp_LU (pc=0x2353a10)
> >> > >>> at /sandbox/hzhang/petsc/src/ksp/pc/impls/factor/lu/lu.c:152
> >> > >>> #11 0x00007f1182b16f24 in PCSetUp (pc=0x2353a10)
> >> > >>> at /sandbox/hzhang/petsc/src/ksp/pc/interface/precon.c:983
> >> > >>> #12 0x00007f1182be61b5 in KSPSetUp (ksp=0x232c2a0)
> >> > >>> at /sandbox/hzhang/petsc/src/ksp/ksp/interface/itfunc.c:332
> >> > >>> #13 0x0000000000405a31 in main (argc=11, args=0x7fff65499578)
> >> > >>> at
> >> /sandbox/hzhang/petsc/src/ksp/ksp/examples/tutorials/ex10.c:312
> >> > >>>
> >> > >>> You may take a look at it. Sequential symbolic factorization works
> >> fine.
> >> > >>>
> >> > >>> Why superlu_dist (v4.0) in complex precision displays
> >> > >>>
> >> > >>> .. Starting with 1 OpenMP threads
> >> > >>> [0] .. BIG U size 1342464
> >> > >>> [0] .. BIG V size 131072
> >> > >>> Max row size is 1311
> >> > >>> Using buffer_size of 5000000
> >> > >>> Threads per process 1
> >> > >>> ...
> >> > >>>
> >> > >>> I realize that I use superlu_dist v4.0. Would v4.1 works? I'll give
> >> it a
> >> > >>> try tomorrow.
> >> > >>>
> >> > >>> Hong
> >> > >>>
> >> > >>> On Mon, Jul 27, 2015 at 1:25 PM, Anthony Paul Haas <
> >> > >>> aph at email.arizona.edu> wrote:
> >> > >>>
> >> > >>>> Hi Hong,
> >> > >>>>
> >> > >>>> No that is not the correct matrix. Note that I forgot to mention
> >> that
> >> > >>>> it is a complex matrix. I tried loading the matrix I sent you this
> >> morning
> >> > >>>> with:
> >> > >>>>
> >> > >>>> !...Load a Matrix in Binary Format
> >> > >>>> call
> >> > >>>>
> >> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Amat_binary.m",FILE_MODE_READ,viewer,ierr)
> >> > >>>> call MatCreate(PETSC_COMM_WORLD,DLOAD,ierr)
> >> > >>>> call MatSetType(DLOAD,MATAIJ,ierr)
> >> > >>>> call MatLoad(DLOAD,viewer,ierr)
> >> > >>>> call PetscViewerDestroy(viewer,ierr)
> >> > >>>>
> >> > >>>> call MatView(DLOAD,PETSC_VIEWER_STDOUT_WORLD,ierr)
> >> > >>>>
> >> > >>>> The first 37 rows should look like this:
> >> > >>>>
> >> > >>>> Mat Object: 2 MPI processes
> >> > >>>> type: mpiaij
> >> > >>>> row 0: (0, 1)
> >> > >>>> row 1: (1, 1)
> >> > >>>> row 2: (2, 1)
> >> > >>>> row 3: (3, 1)
> >> > >>>> row 4: (4, 1)
> >> > >>>> row 5: (5, 1)
> >> > >>>> row 6: (6, 1)
> >> > >>>> row 7: (7, 1)
> >> > >>>> row 8: (8, 1)
> >> > >>>> row 9: (9, 1)
> >> > >>>> row 10: (10, 1)
> >> > >>>> row 11: (11, 1)
> >> > >>>> row 12: (12, 1)
> >> > >>>> row 13: (13, 1)
> >> > >>>> row 14: (14, 1)
> >> > >>>> row 15: (15, 1)
> >> > >>>> row 16: (16, 1)
> >> > >>>> row 17: (17, 1)
> >> > >>>> row 18: (18, 1)
> >> > >>>> row 19: (19, 1)
> >> > >>>> row 20: (20, 1)
> >> > >>>> row 21: (21, 1)
> >> > >>>> row 22: (22, 1)
> >> > >>>> row 23: (23, 1)
> >> > >>>> row 24: (24, 1)
> >> > >>>> row 25: (25, 1)
> >> > >>>> row 26: (26, 1)
> >> > >>>> row 27: (27, 1)
> >> > >>>> row 28: (28, 1)
> >> > >>>> row 29: (29, 1)
> >> > >>>> row 30: (30, 1)
> >> > >>>> row 31: (31, 1)
> >> > >>>> row 32: (32, 1)
> >> > >>>> row 33: (33, 1)
> >> > >>>> row 34: (34, 1)
> >> > >>>> row 35: (35, 1)
> >> > >>>> row 36: (1, -41.2444) (35, -41.2444) (36, 118.049 - 0.999271 i)
> >> (37,
> >> > >>>> -21.447) (38, 5.18873) (39, -2.34856) (40, 1.3607) (41,
> >> -0.898206)
> >> > >>>> (42, 0.642715) (43, -0.48593) (44, 0.382471) (45, -0.310476)
> >> (46,
> >> > >>>> 0.258302) (47, -0.219268) (48, 0.189304) (49, -0.165815) (50,
> >> > >>>> 0.147076) (51, -0.131907) (52, 0.119478) (53, -0.109189) (54,
> >> 0.1006)
> >> > >>>> (55, -0.0933795) (56, 0.0872779) (57, -0.0821019) (58,
> >> 0.0777011) (59,
> >> > >>>> -0.0739575) (60, 0.0707775) (61, -0.0680868) (62, 0.0658258)
> >> (63,
> >> > >>>> -0.0639473) (64, 0.0624137) (65, -0.0611954) (66, 0.0602698)
> >> (67,
> >> > >>>> -0.0596202) (68, 0.0592349) (69, -0.0295536) (71, -21.447)
> >> (106,
> >> > >>>> 5.18873) (141, -2.34856) (176, 1.3607) (211, -0.898206) (246,
> >> > >>>> 0.642715) (281, -0.48593) (316, 0.382471) (351, -0.310476)
> >> (386,
> >> > >>>> 0.258302) (421, -0.219268) (456, 0.189304) (491, -0.165815)
> >> (526,
> >> > >>>> 0.147076) (561, -0.131907) (596, 0.119478) (631, -0.109189)
> >> (666,
> >> > >>>> 0.1006) (701, -0.0933795) (736, 0.0872779) (771, -0.0821019)
> >> (806,
> >> > >>>> 0.0777011) (841, -0.0739575) (876, 0.0707775) (911,
> >> -0.0680868) (946,
> >> > >>>> 0.0658258) (981, -0.0639473) (1016, 0.0624137) (1051,
> >> -0.0611954)
> >> > >>>> (1086, 0.0602698) (1121, -0.0596202) (1156, 0.0592349) (1191,
> >> > >>>> -0.0295536) (1261, 0) (3676, 117.211) (3711, -58.4801) (3746,
> >> > >>>> -78.3633) (3781, 29.4911) (3816, -15.8073) (3851, 9.94324)
> >> (3886,
> >> > >>>> -6.87205) (3921, 5.05774) (3956, -3.89521) (3991, 3.10522)
> >> (4026,
> >> > >>>> -2.54388) (4061, 2.13082) (4096, -1.8182) (4131, 1.57606)
> >> (4166,
> >> > >>>> -1.38491) (4201, 1.23155) (4236, -1.10685) (4271, 1.00428)
> >> (4306,
> >> > >>>> -0.919116) (4341, 0.847829) (4376, -0.787776) (4411, 0.736933)
> >> (4446,
> >> > >>>> -0.693735) (4481, 0.656958) (4516, -0.625638) (4551, 0.599007)
> >> (4586,
> >> > >>>> -0.576454) (4621, 0.557491) (4656, -0.541726) (4691, 0.528849)
> >> (4726,
> >> > >>>> -0.518617) (4761, 0.51084) (4796, -0.50538) (4831, 0.502142)
> >> (4866,
> >> > >>>> -0.250534)
> >> > >>>>
> >> > >>>>
> >> > >>>> Thanks,
> >> > >>>>
> >> > >>>> Anthony
> >> > >>>>
> >> > >>>>
> >> > >>>>
> >> > >>>>
> >> > >>>>
> >> > >>>> On Fri, Jul 24, 2015 at 7:56 PM, Hong <hzhang at mcs.anl.gov> wrote:
> >> > >>>>
> >> > >>>>> Anthony:
> >> > >>>>> I test your Amat_binary.m
> >> > >>>>> using petsc/src/ksp/ksp/examples/tutorials/ex10.c.
> >> > >>>>> Your matrix has many zero rows:
> >> > >>>>> ./ex10 -f0 ~/tmp/Amat_binary.m -rhs 0 -mat_view |more
> >> > >>>>> Mat Object: 1 MPI processes
> >> > >>>>> type: seqaij
> >> > >>>>> row 0: (0, 1)
> >> > >>>>> row 1: (1, 0)
> >> > >>>>> row 2: (2, 1)
> >> > >>>>> row 3: (3, 0)
> >> > >>>>> row 4: (4, 1)
> >> > >>>>> row 5: (5, 0)
> >> > >>>>> row 6: (6, 1)
> >> > >>>>> row 7: (7, 0)
> >> > >>>>> row 8: (8, 1)
> >> > >>>>> row 9: (9, 0)
> >> > >>>>> ...
> >> > >>>>> row 36: (1, 1) (35, 0) (36, 1) (37, 0) (38, 1) (39, 0) (40,
> >> 1)
> >> > >>>>> (41, 0) (42, 1) (43, 0) (44, 1) (45,
> >> > >>>>> 0) (46, 1) (47, 0) (48, 1) (49, 0) (50, 1) (51, 0) (52, 1)
> >> > >>>>> (53, 0) (54, 1) (55, 0) (56, 1) (57, 0)
> >> > >>>>> (58, 1) (59, 0) (60, 1) ...
> >> > >>>>>
> >> > >>>>> Do you send us correct matrix?
> >> > >>>>>
> >> > >>>>>>
> >> > >>>>>> I ran my code through valgrind and gdb as suggested by Barry. I
> >> am
> >> > >>>>>> now coming back to some problem I have had while running with
> >> parallel
> >> > >>>>>> symbolic factorization. I am attaching a test matrix (petsc
> >> binary format)
> >> > >>>>>> that I LU decompose and then use to solve a linear system (see
> >> code below).
> >> > >>>>>> I can run on 2 processors with parsymbfact or with 4 processors
> >> without
> >> > >>>>>> parsymbfact. However, if I run on 4 procs with parsymbfact, the
> >> code is
> >> > >>>>>> just hanging. Below is the simplified test case that I have used
> >> to test.
> >> > >>>>>> The matrix A and B are built somewhere else in my program. The
> >> matrix I am
> >> > >>>>>> attaching is A-sigma*B (see below).
> >> > >>>>>>
> >> > >>>>>> One thing is that I don't know for sparse matrices what is the
> >> > >>>>>> optimum number of processors to use for a LU decomposition? Does
> >> it depend
> >> > >>>>>> on the total number of nonzero? Do you have an easy way to
> >> compute it?
> >> > >>>>>>
> >> > >>>>>
> >> > >>>>> You have to experiment your matrix on a target machine to find
> >> out.
> >> > >>>>>
> >> > >>>>> Hong
> >> > >>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>> Subroutine HowBigLUCanBe(rank)
> >> > >>>>>>
> >> > >>>>>> IMPLICIT NONE
> >> > >>>>>>
> >> > >>>>>> integer(i4b),intent(in) :: rank
> >> > >>>>>> integer(i4b) :: i,ct
> >> > >>>>>> real(dp) :: begin,endd
> >> > >>>>>> complex(dpc) :: sigma
> >> > >>>>>>
> >> > >>>>>> PetscErrorCode ierr
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>> if (rank==0) call cpu_time(begin)
> >> > >>>>>>
> >> > >>>>>> if (rank==0) then
> >> > >>>>>> write(*,*)
> >> > >>>>>> write(*,*)'Testing How Big LU Can Be...'
> >> > >>>>>> write(*,*)'============================'
> >> > >>>>>> write(*,*)
> >> > >>>>>> endif
> >> > >>>>>>
> >> > >>>>>> sigma = (1.0d0,0.0d0)
> >> > >>>>>> call MatAXPY(A,-sigma,B,DIFFERENT_NONZERO_PATTERN,ierr) !
> >> on
> >> > >>>>>> exit A = A-sigma*B
> >> > >>>>>>
> >> > >>>>>> !.....Write Matrix to ASCII and Binary Format
> >> > >>>>>> !call
> >> > >>>>>> PetscViewerASCIIOpen(PETSC_COMM_WORLD,"Amat.m",viewer,ierr)
> >> > >>>>>> !call MatView(DXX,viewer,ierr)
> >> > >>>>>> !call PetscViewerDestroy(viewer,ierr)
> >> > >>>>>>
> >> > >>>>>> call
> >> > >>>>>>
> >> PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Amat_binary.m",FILE_MODE_WRITE,viewer,ierr)
> >> > >>>>>> call MatView(A,viewer,ierr)
> >> > >>>>>> call PetscViewerDestroy(viewer,ierr)
> >> > >>>>>>
> >> > >>>>>> !.....Create Linear Solver Context
> >> > >>>>>> call KSPCreate(PETSC_COMM_WORLD,ksp,ierr)
> >> > >>>>>>
> >> > >>>>>> !.....Set operators. Here the matrix that defines the linear
> >> system
> >> > >>>>>> also serves as the preconditioning matrix.
> >> > >>>>>> !call
> >> KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN,ierr)
> >> > >>>>>> !aha commented and replaced by next line
> >> > >>>>>> call KSPSetOperators(ksp,A,A,ierr) ! remember: here A =
> >> > >>>>>> A-sigma*B
> >> > >>>>>>
> >> > >>>>>> !.....Set Relative and Absolute Tolerances and Uses Default for
> >> > >>>>>> Divergence Tol
> >> > >>>>>> tol = 1.e-10
> >> > >>>>>> call
> >> > >>>>>>
> >> KSPSetTolerances(ksp,tol,tol,PETSC_DEFAULT_REAL,PETSC_DEFAULT_INTEGER,ierr)
> >> > >>>>>>
> >> > >>>>>> !.....Set the Direct (LU) Solver
> >> > >>>>>> call KSPSetType(ksp,KSPPREONLY,ierr)
> >> > >>>>>> call KSPGetPC(ksp,pc,ierr)
> >> > >>>>>> call PCSetType(pc,PCLU,ierr)
> >> > >>>>>> call
> >> PCFactorSetMatSolverPackage(pc,MATSOLVERSUPERLU_DIST,ierr)
> >> > >>>>>> ! MATSOLVERSUPERLU_DIST MATSOLVERMUMPS
> >> > >>>>>>
> >> > >>>>>> !.....Create Right-Hand-Side Vector
> >> > >>>>>> call MatCreateVecs(A,frhs,PETSC_NULL_OBJECT,ierr)
> >> > >>>>>> call MatCreateVecs(A,sol,PETSC_NULL_OBJECT,ierr)
> >> > >>>>>>
> >> > >>>>>> allocate(xwork1(IendA-IstartA))
> >> > >>>>>> allocate(loc(IendA-IstartA))
> >> > >>>>>>
> >> > >>>>>> ct=0
> >> > >>>>>> do i=IstartA,IendA-1
> >> > >>>>>> ct=ct+1
> >> > >>>>>> loc(ct)=i
> >> > >>>>>> xwork1(ct)=(1.0d0,0.0d0)
> >> > >>>>>> enddo
> >> > >>>>>>
> >> > >>>>>> call
> >> > >>>>>> VecSetValues(frhs,IendA-IstartA,loc,xwork1,INSERT_VALUES,ierr)
> >> > >>>>>> call VecZeroEntries(sol,ierr)
> >> > >>>>>>
> >> > >>>>>> deallocate(xwork1,loc)
> >> > >>>>>>
> >> > >>>>>> !.....Assemble Vectors
> >> > >>>>>> call VecAssemblyBegin(frhs,ierr)
> >> > >>>>>> call VecAssemblyEnd(frhs,ierr)
> >> > >>>>>>
> >> > >>>>>> !.....Solve the Linear System
> >> > >>>>>> call KSPSolve(ksp,frhs,sol,ierr)
> >> > >>>>>>
> >> > >>>>>> !call VecView(sol,PETSC_VIEWER_STDOUT_WORLD,ierr)
> >> > >>>>>>
> >> > >>>>>> if (rank==0) then
> >> > >>>>>> call cpu_time(endd)
> >> > >>>>>> write(*,*)
> >> > >>>>>> print '("Total time for HowBigLUCanBe = ",f21.3,"
> >> > >>>>>> seconds.")',endd-begin
> >> > >>>>>> endif
> >> > >>>>>>
> >> > >>>>>> call SlepcFinalize(ierr)
> >> > >>>>>>
> >> > >>>>>> STOP
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>> end Subroutine HowBigLUCanBe
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>> On 07/08/2015 11:23 AM, Xiaoye S. Li wrote:
> >> > >>>>>>
> >> > >>>>>> Indeed, the parallel symbolic factorization routine needs power
> >> of
> >> > >>>>>> 2 processes, however, you can use however many processes you
> >> need;
> >> > >>>>>> internally, we redistribute matrix to nearest power of 2
> >> processes, do
> >> > >>>>>> symbolic, then redistribute back to all the processes to do
> >> factorization,
> >> > >>>>>> triangular solve etc. So, there is no restriction from the
> >> users
> >> > >>>>>> viewpoint.
> >> > >>>>>>
> >> > >>>>>> It's difficult to tell what the problem is. Do you think you
> >> can
> >> > >>>>>> print your matrix, then, I can do some debugging by running
> >> superlu_dist
> >> > >>>>>> standalone?
> >> > >>>>>>
> >> > >>>>>> Sherry
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>> On Wed, Jul 8, 2015 at 10:34 AM, Anthony Paul Haas <
> >> > >>>>>> aph at email.arizona.edu> wrote:
> >> > >>>>>>
> >> > >>>>>>> Hi,
> >> > >>>>>>>
> >> > >>>>>>> I have used the switch -mat_superlu_dist_parsymbfact in my pbs
> >> > >>>>>>> script. However, although my program worked fine with
> >> sequential symbolic
> >> > >>>>>>> factorization, I get one of the following 2 behaviors when I
> >> run with
> >> > >>>>>>> parallel symbolic factorization (depending on the number of
> >> processors that
> >> > >>>>>>> I use):
> >> > >>>>>>>
> >> > >>>>>>> 1) the program just hangs (it seems stuck in some subroutine
> >> ==>
> >> > >>>>>>> see test.out-hangs)
> >> > >>>>>>> 2) I get a floating point exception ==> see
> >> > >>>>>>> test.out-floating-point-exception
> >> > >>>>>>>
> >> > >>>>>>> Note that as suggested in the Superlu manual, I use a power of
> >> 2
> >> > >>>>>>> number of procs. Are there any tunable parameters for the
> >> parallel symbolic
> >> > >>>>>>> factorization? Note that when I build my sparse matrix, most
> >> elements I add
> >> > >>>>>>> are nonzero of course but to simplify the programming, I also
> >> add a few
> >> > >>>>>>> zero elements in the sparse matrix. I was thinking that maybe
> >> if the
> >> > >>>>>>> parallel symbolic factorization proceed by block, there could
> >> be some
> >> > >>>>>>> blocks where the pivot would be zero, hence creating the FPE??
> >> > >>>>>>>
> >> > >>>>>>> Thanks,
> >> > >>>>>>>
> >> > >>>>>>> Anthony
> >> > >>>>>>>
> >> > >>>>>>>
> >> > >>>>>>>
> >> > >>>>>>> On Wed, Jul 8, 2015 at 6:46 AM, Xiaoye S. Li <xsli at lbl.gov>
> >> wrote:
> >> > >>>>>>>
> >> > >>>>>>>> Did you find out how to change option to use parallel symbolic
> >> > >>>>>>>> factorization? Perhaps PETSc team can help.
> >> > >>>>>>>>
> >> > >>>>>>>> Sherry
> >> > >>>>>>>>
> >> > >>>>>>>>
> >> > >>>>>>>> On Tue, Jul 7, 2015 at 3:58 PM, Xiaoye S. Li <xsli at lbl.gov>
> >> wrote:
> >> > >>>>>>>>
> >> > >>>>>>>>> Is there an inquiry function that tells you all the available
> >> > >>>>>>>>> options?
> >> > >>>>>>>>>
> >> > >>>>>>>>> Sherry
> >> > >>>>>>>>>
> >> > >>>>>>>>> On Tue, Jul 7, 2015 at 3:25 PM, Anthony Paul Haas <
> >> > >>>>>>>>> aph at email.arizona.edu> wrote:
> >> > >>>>>>>>>
> >> > >>>>>>>>>> Hi Sherry,
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> Thanks for your message. I have used superlu_dist default
> >> > >>>>>>>>>> options. I did not realize that I was doing serial symbolic
> >> factorization.
> >> > >>>>>>>>>> That is probably the cause of my problem.
> >> > >>>>>>>>>> Each node on Garnet has 60GB usable memory and I can run
> >> with
> >> > >>>>>>>>>> 1,2,4,8,16 or 32 core per node.
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> So I should use:
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> -mat_superlu_dist_r 20
> >> > >>>>>>>>>> -mat_superlu_dist_c 32
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> How do you specify the parallel symbolic factorization
> >> option?
> >> > >>>>>>>>>> is it -mat_superlu_dist_matinput 1
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> Thanks,
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> Anthony
> >> > >>>>>>>>>>
> >> > >>>>>>>>>>
> >> > >>>>>>>>>> On Tue, Jul 7, 2015 at 3:08 PM, Xiaoye S. Li <xsli at lbl.gov>
> >> > >>>>>>>>>> wrote:
> >> > >>>>>>>>>>
> >> > >>>>>>>>>>> For superlu_dist failure, this occurs during symbolic
> >> > >>>>>>>>>>> factorization. Since you are using serial symbolic
> >> factorization, it
> >> > >>>>>>>>>>> requires the entire graph of A to be available in the
> >> memory of one MPI
> >> > >>>>>>>>>>> task. How much memory do you have for each MPI task?
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>> It won't help even if you use more processes. You should
> >> try
> >> > >>>>>>>>>>> to use parallel symbolic factorization option.
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>> Another point. You set up process grid as:
> >> > >>>>>>>>>>> Process grid nprow 32 x npcol 20
> >> > >>>>>>>>>>> For better performance, you show swap the grid dimension.
> >> That
> >> > >>>>>>>>>>> is, it's better to use 20 x 32, never gives nprow larger
> >> than npcol.
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>> Sherry
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>> On Tue, Jul 7, 2015 at 1:27 PM, Barry Smith <
> >> bsmith at mcs.anl.gov>
> >> > >>>>>>>>>>> wrote:
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>>>
> >> > >>>>>>>>>>>> I would suggest running a sequence of problems, 101 by
> >> 101
> >> > >>>>>>>>>>>> 111 by 111 etc and get the memory usage in each case (when
> >> you run out of
> >> > >>>>>>>>>>>> memory you can get NO useful information out about memory
> >> needs). You can
> >> > >>>>>>>>>>>> then plot memory usage as a function of problem size to
> >> get a handle on how
> >> > >>>>>>>>>>>> much memory it is using. You can also run on more and
> >> more processes
> >> > >>>>>>>>>>>> (which have a total of more memory) to see how large a
> >> problem you may be
> >> > >>>>>>>>>>>> able to reach.
> >> > >>>>>>>>>>>>
> >> > >>>>>>>>>>>> MUMPS also has an "out of core" version (which we have
> >> never
> >> > >>>>>>>>>>>> used) that could in theory anyways let you get to large
> >> problems if you
> >> > >>>>>>>>>>>> have lots of disk space, but you are on your own figuring
> >> out how to use it.
> >> > >>>>>>>>>>>>
> >> > >>>>>>>>>>>> Barry
> >> > >>>>>>>>>>>>
> >> > >>>>>>>>>>>> > On Jul 7, 2015, at 2:37 PM, Anthony Paul Haas <
> >> > >>>>>>>>>>>> aph at email.arizona.edu> wrote:
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > Hi Jose,
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > In my code, I use once PETSc to solve a linear system to
> >> get
> >> > >>>>>>>>>>>> the baseflow (without using SLEPc) and then I use SLEPc to
> >> do the stability
> >> > >>>>>>>>>>>> analysis of that baseflow. This is why, there are some
> >> SLEPc options that
> >> > >>>>>>>>>>>> are not used in test.out-superlu_dist-151x151 (when I am
> >> solving for the
> >> > >>>>>>>>>>>> baseflow with PETSc only). I have attached a 101x101 case
> >> for which I get
> >> > >>>>>>>>>>>> the eigenvalues. That case works fine. However If i
> >> increase to 151x151, I
> >> > >>>>>>>>>>>> get the error that you can see in
> >> test.out-superlu_dist-151x151 (similar
> >> > >>>>>>>>>>>> error with mumps: see test.out-mumps-151x151 line 2918 ).
> >> If you look a the
> >> > >>>>>>>>>>>> very end of the files test.out-superlu_dist-151x151 and
> >> > >>>>>>>>>>>> test.out-mumps-151x151, you will see that the last info
> >> message printed is:
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > On Processor (after EPSSetFromOptions) 0 memory:
> >> > >>>>>>>>>>>> 0.65073152000E+08 =====> (see line 807 of
> >> module_petsc.F90)
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > This means that the memory error probably occurs in the
> >> call
> >> > >>>>>>>>>>>> to EPSSolve (see module_petsc.F90 line 810). I would like
> >> to evaluate how
> >> > >>>>>>>>>>>> much memory is required by the most memory intensive
> >> operation within
> >> > >>>>>>>>>>>> EPSSolve. Since I am solving a generalized EVP, I would
> >> imagine that it
> >> > >>>>>>>>>>>> would be the LU decomposition. But is there an accurate
> >> way of doing it?
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > Before starting with iterative solvers, I would like to
> >> > >>>>>>>>>>>> exploit as much as I can direct solvers. I tried GMRES
> >> with default
> >> > >>>>>>>>>>>> preconditioner at some point but I had convergence
> >> problem. What
> >> > >>>>>>>>>>>> solver/preconditioner would you recommend for a
> >> generalized non-Hermitian
> >> > >>>>>>>>>>>> (EPS_GNHEP) EVP?
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > Thanks,
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > Anthony
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > On Tue, Jul 7, 2015 at 12:17 AM, Jose E. Roman <
> >> > >>>>>>>>>>>> jroman at dsic.upv.es> wrote:
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > El 07/07/2015, a las 02:33, Anthony Haas escribió:
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > > Hi,
> >> > >>>>>>>>>>>> > >
> >> > >>>>>>>>>>>> > > I am computing eigenvalues using PETSc/SLEPc and
> >> > >>>>>>>>>>>> superlu_dist for the LU decomposition (my problem is a
> >> generalized
> >> > >>>>>>>>>>>> eigenvalue problem). The code runs fine for a grid with
> >> 101x101 but when I
> >> > >>>>>>>>>>>> increase to 151x151, I get the following error:
> >> > >>>>>>>>>>>> > >
> >> > >>>>>>>>>>>> > > Can't expand MemType 1: jcol 16104 (and then [NID
> >> 00037]
> >> > >>>>>>>>>>>> 2015-07-06 19:19:17 Apid 31025976: OOM killer terminated
> >> this process.)
> >> > >>>>>>>>>>>> > >
> >> > >>>>>>>>>>>> > > It seems to be a memory problem. I monitor the memory
> >> usage
> >> > >>>>>>>>>>>> as far as I can and it seems that memory usage is pretty
> >> low. The most
> >> > >>>>>>>>>>>> memory intensive part of the program is probably the LU
> >> decomposition in
> >> > >>>>>>>>>>>> the context of the generalized EVP. Is there a way to
> >> evaluate how much
> >> > >>>>>>>>>>>> memory will be required for that step? I am currently
> >> running the debug
> >> > >>>>>>>>>>>> version of the code which I would assume would use more
> >> memory?
> >> > >>>>>>>>>>>> > >
> >> > >>>>>>>>>>>> > > I have attached the output of the job. Note that the
> >> > >>>>>>>>>>>> program uses twice PETSc: 1) to solve a linear system for
> >> which no problem
> >> > >>>>>>>>>>>> occurs, and, 2) to solve the Generalized EVP with SLEPc,
> >> where I get the
> >> > >>>>>>>>>>>> error.
> >> > >>>>>>>>>>>> > >
> >> > >>>>>>>>>>>> > > Thanks
> >> > >>>>>>>>>>>> > >
> >> > >>>>>>>>>>>> > > Anthony
> >> > >>>>>>>>>>>> > > <test.out-superlu_dist-151x151>
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > In the output you are attaching there are no SLEPc
> >> objects in
> >> > >>>>>>>>>>>> the report and SLEPc options are not used. It seems that
> >> SLEPc calls are
> >> > >>>>>>>>>>>> skipped?
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > Do you get the same error with MUMPS? Have you tried to
> >> solve
> >> > >>>>>>>>>>>> linear systems with a preconditioned iterative solver?
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> > Jose
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>> >
> >> > >>>>>>>>>>>>
> >> <module_petsc.F90><test.out-mumps-151x151><test.out_superlu_dist-101x101><test.out-superlu_dist-151x151>
> >> > >>>>>>>>>>>>
> >> > >>>>>>>>>>>>
> >> > >>>>>>>>>>>
> >> > >>>>>>>>>>
> >> > >>>>>>>>>
> >> > >>>>>>>>
> >> > >>>>>>>
> >> > >>>>>>
> >> > >>>>>>
> >> > >>>>>
> >> > >>>>
> >> > >>>
> >> > >>
> >> > >
> >> >
> >>
> >
> >
>
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